Welcome to the forum, Noek!
The statement that you haven't changed anything is what has me really wondering, as there are a few things that typically are the cause - but those are due to set up. I'll mention them anyway, as perhaps someone changed a setting on accident.
If there isn't a lot of low frequency content, and your other speakers are set to large, then the sub might not get much signal. MCACC seems to set speakers to "large" even when they are really aren't, so make sure the speaker sizes are what you want (especially because you just went through that setup again).
If the output level from the receiver to the subwoofer is pretty low (e.g. "-5 dB"), then there might not be enough signal to trigger the auto-on feature on a sub. If your sub is set to turn on and off automatically, try setting it to be always on to check if that's the reason. If it is, then you can lower the volume setting on the subwoofer itself (to lower the gain on the sub's internal amp) and rerun MCACC. This will result in a higher signal level going to the sub to get the same output with a lower gain on the subwoofer's amp.
You already swapped out the cable, which can be a cause. The connections at the ends of a cable can get loose over time, resulting in intermittent loss of signal.
That's what comes to mind right now.